8VF4 | pdb_00008vf4

CryoEM structure of Ku homodimer super-complex with hairpin DNA

• PDB DOI: https://doi.org/10.2210/pdb8VF4/pdb
• NAKB: 8VF4
• EM Map EMD-43185: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycobacterium tuberculosis H37Rv, saltans group
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-21 Released: 2025-12-10 
• Deposition Author(s): Baral, J., Rouiller, I., Das, A.K.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Science and Engineering Research Board (SERB)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Bringing the ends together: cryo-EM structures of mycobacterial Ku in complex with DNA define its role in NHEJ synapsis.

Baral, J., Ang, C.S., McMillan, P.J., Shobhana, K., Saini, A., Hinde, E., Das, A.K., Rouiller, I.

(2026) Nucleic Acids Res 54

• PubMed: 41521670 
• DOI: https://doi.org/10.1093/nar/gkaf1418
• Primary Citation Related Structures: 
  8V53, 8VF2, 8VF4, 8VF5


• PubMed Abstract: 
  

  Non-homologous end joining (NHEJ) is the sole pathway for repairing double-strand breaks in Mycobacterium tuberculosis during dormancy, relying on mycobacterial Ku (mKu) and ligase D, with mKu as the rate-limiting factor. Despite its essential role, the lack of structural information on prokaryotic Ku has hindered understanding of the molecular mechanisms underlying bacterial two-component NHEJ machinery. Here, we present the first cryo-electron microscopy (cryo-EM) structures of mKu in DNA-bound and higher-order supercomplex forms, revealing a Ku-mediated DNA synapsis mechanism unique to prokaryotes. Integrating cryo-EM with hydrogen-deuterium exchange mass spectrometry, we define key mKu-mKu dimerization, DNA-binding, and synapsis interactions essential for efficient NHEJ, bridging structure with function. Structure-guided in silico mutagenesis, coupled with electrophoretic mobility shift assays, identifies residues essential for DNA binding and synaptic assembly, which are crucial for NHEJ. Förster resonance energy transfer confirms DNA-dependent mKu oligomerization in solution, while live-cell imaging captures its spatiotemporal dynamics during double-stranded DNA break repair. These findings provide fundamental insights into the architecture and function of prokaryotic NHEJ, positioning mKu as a potential therapeutic target against tuberculosis and offering a framework for understanding DNA repair across bacterial species.

---

Organizational Affiliation: 
• Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, West Midnapore 721302, West Bengal, India.
School of Physics, University of Melbourne, Victoria 3010, Australia.
Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia.
Australian Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins, Parkville, Victoria 3052, Australia.
Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3052, Australia.
Biological Optical Microscopy Platform, University of Melbourne, Victoria 3010, Australia.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 252.16 kDa 
• Atom Count: 12,777 
• Modeled Residue Count: 1,449 
• Deposited Residue Count: 1,935 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-homologous end joining protein Ku	A, B, I, J, K, L	295	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: mku, Rv0937c
UniProt
Find proteins for P9WKD9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKD9  Go to UniProtKB:  P9WKD9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (21-mer)	C, E, G	21	saltans group

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (34-MER)	D, F, H	34	saltans group

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Baral, J., Rouiller, I., Das, A.K.

---

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP2000934
Science and Engineering Research Board (SERB)	India	CRG/2020/002622

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release
  
• Version 1.1: 2026-04-08
  Changes: Data collection, Database references